Prototype: The Father
by Grimankin
Summary: After the Manhattan incident was over Alex Mercer thought normal life would ensue, but while on a simple walk he encounters a new kind of infected. What will be the result of this encounter and who is this "Father" they think of?
1. Chapter 1

AN: *puts on a fancy white suit and coat and a pair of round glasses. Also has a maniacal stare* My friends, it has often been said that I like **[Prototype]. **My friends - I like **[Prototype]**. No... friends - I LOVE **[Prototype]**! I love punches, I love kicks, consuming, becoming, claws, whipfists, muscle masses, blades, air strikes and fly-kicking gunships. *rambles on how he loves all the things about Prototype for 7 minutes.*

Okay, now that that's over with you know why I wanted to post this little thing here. Also - cookies to people who understood the reference above.*wink*  
>While I loved most of the Prototype crossovers and fanfics I found most of them have a rather cold and heroic Alex Mercer. Sure - he's says he's the virus and all but still wants to be human and saves the day from Blackwatch and stuff. So here's a little bit of my own "something different" stuff.<p>

I hope you enjoy this little thing here. I got chapter 1 finished already, but I'll be posting it a bit later - when I do a bit of chapter 2.

Hope you enjoy this.

Oh and DISCLAMER: I don't own Prototype. If I did Dana Mercer would be out of coma and infected with Blacklight, as well as Alex.**  
><strong>

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><p><strong>Prototype: The Father.<strong>

Prologue: "Aftermath"

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><p><em>- Look at your handiwork now.<br>-Oh yeah, they're headless – an infected army without a leader… it's only a matter of time before they're wiped out.  
>-And if the are other leaders out there?<br>-No… they're all dead… all dead… except me._

_He grinned_

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><p><strong>[Alex Mercer POV]<strong>

The Manhattan Incident. The horrible event had been written into the world's history with blood, suffering and thousands if not millions of casualties. But the virus was stopped, the infected almost all now killed, the truth covered up… well, partially. The official story goes like this – a genius doctor and genetics professor became the world's most infamous terrorist. The man unleashed the horrible, unknown virus that claimed the city while the he himself escaped into hiding and is yet to found. The man was also responsible for the nuclear explosion offshore, which failed only due to the sacrifices and sense of duty of the Military.  
>No names were involved besides Mercer – no Blackwatch, no GenTek, no Redlight, no Elizabeth Greene.<p>

Five months have passed since I put an end to all that, and the city is being still restored. The virus was stopped and only a few infected are still around in the sewers or abandoned buildings and are usually found during repairs, which are no short of being major repairs. What about me? I've killed everyone I had to. Karen Parker, Peter Randall, Robert Cross and the infected – all of them. I left the infected army without a leader by killing all of those who had any kind of ability for individual thought. Since then I stayed low, not causing any trouble, living under a different name, a different face.  
>I am not Alexander Mercer – I am the Blacklight virus. But at the same time I can't deny that his body and his memories are the original me, in a way. It would be hard to explain to anyone.<p>

Dana? She… didn't wake up yet. Doctor Bradley Ragland is still taking care of her to his best abilities, and since the end of the incident he stopped having any kind of pressure from the deceased McMullen or any of his superiors. He was even hired by a 2nd leading Genetics Company in the world… I forgot its name, but it's really simple.  
>When she wakes up… I don't know… I have no idea what we are going to talk about. Her life and our relationship will never be the same again. She knows who – no – what I am now. I won't run away when she does wake up and we will talk. I'll see what comes out of that…<p>

Today started out like it always does. I woke up from sleep early in the evening. Actually I don't need sleep like humans do, but habits die hard and I take some satisfaction in sleeping, in having peace for some time, while my body and mind are shut off in deep sleep-like trance. I see no dreams while asleep and perhaps that's even better than if I did. Those wouldn't be the best dreams I'd see. After waking up I drink a cup of coffee, which is as needed as sleep is – and that means it's not needed at all… I just take some kind of pleasure in doing these things. Perhaps… they make me feel human again, or rather human at all – since I was never a human to begin with, even though I drank billions of coffee cups and had billions of dreams. I fell in love thousands of times and made love as many times, if not more. All the lives I took – everyone I consumed – they all live within me as memories and experiences of those countless people. Simple men and women, soldiers, businessmen, pilots, janitors, teachers and who knows who else.

After having my usual coffee I begin to roam the streets, observing the humans live on. The voices and screams inside me never cease except for when I sleeps, so all the time I am awake I can hear them. They torture my mind and soul… if I even have one, but as time passes I find them to be less and less loud. I guess that means I'm getting used to them – that's all.

There's nothing much else for me to say. I no longer do anything but exist. All that's left for me is to do that and consume occasional people to sustain myself. That was… until earlier today.

I was walking through the city streets like I always did, my hands resting inside the pockets of my jacket, since today I decided to go around in my "original" form. And while doing so I heard something. A screeching sound mixed with a roar – a thing only an infected could emit. I decided to check it out and find the source. After I made a turn at the nearest corner I found it – a wounded infected which looked very weird. It resembled a human more than other infected did, yet it was less twisted and seemed to have a spark of intelligence in it's eyes. The second it saw me it got off the ground and ran for it, with speed that rivaled a hunter. I followed, easily jumping over and running over small obstacles until I saw it break a sewer entrance and dive down – so did I.  
>As I landed I switched to the infected vision, as I called it, and scanned the surroundings for it. I saw it running away and kept pursuing it down, lower and lower, until we finally reached some old subway station, which was currently abandoned and unused.<p>

There wasn't much afterwards – we fought and the creature had enough strength left to land a few hits on me, as well as call a few hunters to its aid, which were nearby. I was almost scared for a moment, but not because of its power – but because of the fact that it could control the other infected. A trait only the Hunter Leaders and Greene showed. If another one like Elizabeth Greene would show up – that would only mean a few viral outbreak, more Blackwatch and more casualties. It was not something I wanted.  
>So I killed it, and not only that – I had consumed it. I wanted to know, I needed to know how it became or was "born" this way.<p>

So… down there at the abandoned subway station it became a part of me. It was then that I had relived the moment of my connection to the Hivemind – a thing that was mostly gone without the Mother there to guide them. Truth be told I was never really connected to that thing, and what I did was tap into it, tune in into the voices – just like I did with the Military radio frequencies. But after nearly killing and consuming that thing I finally truly connected with the infected collective intelligence. That Hivemind.

I heard hundreds of voices, all screaming and whispering. The visions I experienced then and there were crystal-clear, unlike most others I had. The voices got so loud and unbearable that I screamed loudly, telling them to "shut the fuck up"… and they did. After a moment thought they voiced themselves again. This time they spoke out in unison – all that current of voices spoke out one single word, putting all the emotions they perhaps had all this time into the single, pleading scream. It was…

"_Faaaatheeer!"_

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><p>AN: Not quite what you thought it would be, yes? Or was it kinda predictable? You can review, but it's not mandatory, and I understand if it... you know... shuckz.<em><br>_


	2. Chapter 2

AN: PSYCHE! Fooled ya, didn't I? Ah... actually I guess not since you could see the chapter two being there since there was a "next" button. Anyways - this is actually chapter 1, but meh - I decided to call it chapter 2 to avoid mixups, so, basically, Prologue is chapter 1.  
>Introducing dem OC's and a 2nd Main Char of the story.<p>

I know this is gonna look a bit weird, but no copycatting and such intended. Prototype just uses the best plot idea possible. Yay for angry, batshit insane gansta Heller who out for revenge!

Enjoy.

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><p><strong>Prototype: The Father<strong>

Chapter 2: "Enter, Blackwatch"

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><p>[3rd Person POV]<p>

The Captain looked around, noticing that the Sergeants had arrived.

"Sergeant Angela Smith, reporting in, sir!" – a woman in black military uniform saluted. The woman looked to be around 25 years old; she had blond hair in a casual short straight hairstyle. The woman wore a personalized blackwatch army suit, which made her slender and fit figure quite visible, as if to underline that she is a woman. Her face was quite beautiful and symmetrical with the only exception of her slightly pointed nose, which, if was shorter would made her face look perfect. Her eyes were emerald-green and her face had the expression of being serious, yet somewhat joyful at the same time, which in her case fit her perfectly.

"Sergeant Harold Right, reporting in, sir!" – a man next to Angela spoke out, saluting. This man was too dressed in blackwatch uniform, just like the rest of the group, though his uniform was a male one. The man looked around 28 years old, he had brown hair, which had no particular hairstyle aside from being short, wavy and swept back, opening his forehead. Harold's eyes were dark-blue. Out of his facial features a square-shaped chin was the only thing that stood out, giving him a stern and dead-serious expression, coupled with his thin lips, which were always kept as a line. The man rarely smiled, even at the funniest of jokes.

"Sergeant Patrick Rogers, reporting in too, sir!" – the next man spoke. He looked about the same age as Angela. His hair was rave-black and swept back too, almost completely, reaching down almost to his neck. This man had a lady-killer face, not too tough-looking, yet not too soft, which he often used, coupled with his fun-loving personality. Even now there was a wide smile on his face, showing his perfectly white teeth. His eyes were brown.

"Sergeant Samantha Noble, sir!" – the second woman in the group spoke out. She looked about 30 years old, her hair was bright-red and her hairstyle was similar to Angela's because she couldn't grow them longer, yet she was known to have her hair down to her back before. Her eyes were gray. Her expression was nearly as dead-serious as Harold's, and she looked like she was the best out of all the group… and actually she was, in both physical skills and wits. She was the unofficial leader of the Sergeant group now standing before the Captain. Her suit was even more figure-fitting that Angela's and it was a wonder how the other soldiers kept their wits about them still.

"Sergeant Frank Black, reporting in, sir!" – the last of the five saluted. The man looked around 24 to 25 year old and was the "youngest" of the five Sergeants. His hair was black as well, with a formal medium straight haircut. His eyes were dark as well, almost black, and due to this nearly blending in with the pupils of his eyes. He was the less fit looking of the group and the shortest, while Haorld being the tallest. The most notable about Frank was that he was actually completely un-notable – grey and ordinary in appearance. His eyes, however, were always cold and hostile, even when smiling or joking around.

The Captain looked all of them over once again, noting every last detail and replaying their personal files in his mind as he always did, and then he finally spoke.

"Okay ladies and gentlemen. It's time for the LEGION team to move out. Your objective is this: we are deploying you near one of the major Red Zones and you are to hold your ground and not let any infected hostiles out, as well as not let any civilians in. The new WISEMAN team will be going into the heart of that Red Zone and will take out the Hive, while you guys defend the West line. Any questions?" – the Captain raised an eyebrow as if someone already asked a stupid question.

"Sir!" – Patrick spoke up. – "Why do we go guard the perimeter while the newbies go in and get all the fun, sir?" – the man smile widened as he finished his question.

"Because, Rogers.." – the Captain sighed. – "… they need to go through trial by fire, and they are gonna get hit in case anything out of the ordinary happens. For all we know there might be something new out there in those Hives. We've had 8 months of fucking peace and quiet and now these damn infected are starting their shit again. There's no way that an event like that could just 'happen' so Red Crown wants us to be ready on all fronts – we have renewed the quarantine and readied the forces." – the man raised his hand and clenched his fist. Everyone knew where this was heading – end of briefing.

"_When we hunt, we kill!  
>No one is safe!<br>Nothing is sacred!  
>We are Blackwatch!<br>We are the last line of defense!  
>We will burn our own to hold the red line; it is the last line to ever hold!<em>_"_

The words sounded through the room as the chorus of 6 men recited the code and credo of their organization. The briefing was over and then men quickly donned on their masks, heading towards the Blackhawk transport helicopters. The whole LEGION team actually counted for more than 200 men, but for this operation required about 40 soldiers, excluding the 5 Sergeants. All of the soldiers had different weapons, but all the Sergeants had the M4's, except Sgt. Right, who had a M294 machine gun. Once everyone boarded the helicopters – they took off.

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><p>Angela was sitting in one of the Blackhawks. With her vest, mask and goggles on she could barely feel the wind except the slight sensation of it as they flew. She was sitting in one of the seats closest to the railings and used the position to look out and observe the city from up high. She used her right hand to hold on to the railing above her and leaned to her left, showing her head out of the helicopter. The city was pretty much the same as she saw it all these days. As they flew through the Blue Zone there was no signs of infected or the chaos that ensued in the other parts of the town. Soon the skyscrapers ended and the lower buildings showed themselves. Down there in the front Angela could see the smoke rising above the roofs of the buildings and whole blocks were shrouded with light red fog.<br>She cursed in her mind and out loud at whoever and whatever made the virus wake up again. She had gone through enough hell back when the first and the second outbreaks happened, but a third time? Oh hell no – she wasn't going to stand this much longer. She was going to go in there and bust all those ugly infected asses back into whatever shithole they came out of!

Angela noticed that a few Apache's flew by, catching a bit of radio chatter. These 3 gunships were a strike team, and they were heading towards the same destination. Well that meant only one thing – problems. Those were either a large number of Hunters or an even larger number of infected. She woman sighed and turned back towards her team. Opposite her sat Sgt. Black, while all the other places were occupied by privates, as well as the two railings, which the few used as steps, while they sat on the Blackhawks floor. Oh and there were these two guys by the gun-turrets on each side too. All in all – there were two helicopters and 20 soldiers each.  
>Angela leaned back on her seat and turned on the comm with her team.<p>

"Okay team, listen up. We gotta hold the West line of the Red Zone for as long as it takes and make sure nothing gets in or gets out. We are authorized to shoot anything or anyone who tries, unless they are Military and have a pass to do so. Now I know we have a few hots-shots but keep your bullets for the infected – I don't want any civilian casualties unless they can't be avoided. I'm sure Sgt. Noble agrees, right?" – she smiled under her mask.

"Positive." – was the only thing Samantha replied with, but that was enough for the team. Across from Angela, Frank nodded and checked his gun again. Whether he was pleased with the results remained unknown, seeing as his face was covered, but he did so only once, and that meant that the M4 worked – that was all that needed. Although Black was a bit of a perfectionist – so who knew?  
>Angela once again looked out and addressed the pilot through the comm.<p>

"How long till landing?" – she asked, a bit bored from waiting. Her gaze went across the roofs from right to left and then backwards.

"About 5 minutes, ma'am." – came the reply.

Okay – all she had to do was wait until they touched the ground.

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><p>[30 minutes later]<p>

It was quiet. Too quiet. Like all life was gone from the street they were stationed at. The team was currently taking position on one of the roadblocks in the middle of the street, on a wall built by the Military forces – one with all the searchlights and barbed wire and all that shit. The metal doors were closed and an APC was parked just behind them, so that no nasty Hunter could get through right away – even if they managed to take down the door. Angela had doubts about that though – they'd just jump over the wall and be done with it. But that's why the turrets were deployed on the walls, along with the machine guns and all the soldiers – nothing gets out and nothing goes in. Only 4 men were on the other side, watching in case of civilians. They would be plenty enough to stop any vehicle or man.

Angela sighed and squatted down, pulling out a pack of cigarettes out of one of the pockets of her armor. She watched the empty road ahead, tracing newspaper as it flew by from one side of the street to the other, while she took out a single cigarette from the pack and reached for the lighter. Once the deed was done she had a lighted cigarette in her mouth, smoke steadily coming from its tip. She hated smoking – but hey, once you get doing this shit you can't quit, unless you got the will to do it. She had the will… she just had no wish to quit, even though she hated smoking because of the smell. A paradox.  
>The girl cracked her neck left and right and stood up, glancing over the others. Everyone looked like they were taking it slow and relaxing, but she knew that once something happened – these trained soldiers, picked out from the best the Army had to offer, would react the very second it did. It was the same for her.<p>

The cigarette was finished and Angela sent the remains flying towards the Hive. Well it didn't make it **that** far, of course, landing not too far away from the wall.

"We have movement" – suddenly the radio came to life, startling Angela a bit. – "A single Military is approaching from the safe side. Orders?"

"Check him for clearance and documents. If there's something wrong with him – shoot to kill." – came orders from Samantha Noble over the comm. _Damn girl – it's like you got no heart._ Was all Angela thought before the Officer in question rushed over. The woman could clearly see the white Blackwatch Officer uniform from here.  
>She tuned in the needed frequency to hear the conversation, and she suspected so did all the other Sergeants.<p>

"Sir, we need to check your documents and clearance before you go any further." – one of the soldiers raised his hand while the other 3 pointed their guns at the Officer.

"Sure, private – here they are." – the guy in question took his ID out of the pocket and handed it to the one who spoke to him. After a few seconds of tension and quiet the soldier gave the documents back. – "Everything seems in order, Lieutenant Rush, sir." – the 4 saluted.

"At ease, boys. I need to speak to your commanders." – came the reply. The others motioned towards the wall and Officer Rush headed towards it. It took him less than 2 minutes to get there and climb up. The five Sergeants gathered before him and each introduced himself and herself. Angela was the last one to do so, and after than was done she sat back on the edge of the wall, carefully positioning herself so not to place her back to the barbed wires.  
>She listened to the small talk with little interest. Why was this guy even here? She didn't know – and cared little. So far this mission was just sitting back and enjoying the quiet. Then Angela decided to listen attentively after all.<p>

".. and that's about it. I'm what you call a 'simple check-up'. The Command didn't even give me any escort." – Rush complained. Angela looked back at Samantha who was listening closely and noticed the woman gripped her M4 tighter. Weird. She spoke next. – "I see. Lieutenant Rush… there's just one thing – I remember there was a Lt. with that name in the WISEMAN team led by Captain Cross. He was reported as KIA."

The whole wall went silent after those words. The Officer tilted his head a bit and exhaled. – "Shit. Didn't think of that." – and the man suddenly jumped backwards, off the wall, with a single backflip. He landed down on the pavement and his arms began to change. A swarm of black-red tendrils covered his hands down from the shoulders and the soldiers saw that they transformed into two 'whipfists'. The man, which turned out to be a monster then proceeded to grab the two closest to him and threw one into the soldiers looking down at him from the top of the wall, while using the other as a weapon, swinging his long arm and smashing the victim's body into the other 2 standing nearby. Angela had only so much time to roll out of the way before the few aside her were knocked back by the flying soldier that hit them, sending the 5 bodies flying, bones cracking and limbs flailing through the air. Most of them were killed on impact – so strong it was.

Just a moment later he landed back on the wall, both his hands shifted into claws. Then the Officer proceeded to slash away at the closest few, somehow sparing Sgt. Black as he did. The latter was grabbed and thrown away like some kind of broken toy, smashing forcefully into the edge of the wall – it was a miracle he didn't fly over it. Finally the enemy shifted entirely into a mass of black-red tentacles which then formed into a man. He was dressed in grey jeans, black jacket, black shoes and a grey hoodie – grey-blue eyes stared coldly from beneath the shadow of the hood, the man's face had a slight smirk across it.  
>Almost all of the squad was already down and Angela was still lying on the floor. It all happened in seconds – hell, even her – a trained soldier had no idea what to do. Samantha apparently had as Angela heard her voice. – "Red Crown, requesting a strike pa-" – she was cut loose as a single red-black tentacle pierced the middle of her chest, pushing out the air from within her lungs.<p>

"Now-now – can't have you calling for backup if I want this thing going smooth." – Alex Mercer's words were like thunder on a cloudless, blue sky. Angela was already up and she began to squeeze the trigger of her gun, aiming it straight at the man's head, when she saw another tentacle burst out of him. The thing hit her straight in the middle of the chest, paralyzing her. The woman could see 3 more tentacles slam into the chests of the other Sergeants, incapacitating them. The man turned slightly, and she felt and saw something like a substance going through the tentacles, injecting itself into her body. She felt great pain and agony while the man smirked a bit wider, a glint of satisfaction in his eyes evident to all but those who were currently impaled. The creature was shot through with dozens of bullets, which seemed to have no affect on his health at all like it was a light itch one could ignore.

When the pain slightly resided Angela lowered her head and saw something else going through the tentacles. Something made Harold scream again, then Samantha, then Patrick and finally Frank. It was her turn. She could see ZEUS' gaze turn to her and then fire erupted from behind him, sending him away, and the tentacle ripping out of her flesh.

The agony made everything turn black.

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><p>AN: So you can pretty much guess what's gunna happen, huh? Cookies to people who read. More cookies to those who actually Review. And search Youtube for this "<strong>Prototype- Mystery of Alex Mercer<strong>". The vid is sooooo kick-ass. Go watch it - NAO!


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